GOLGA6C

golgin A6 family member C, the group of Golgin related

Basic information

Region (hg38): 15:75258334-75273455

Links

ENSG00000167195 ∙ NCBI:653641 ∙ ∙ HGNC:32206 ∙ Uniprot:A6NDK9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GOLGA6C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLGA6C gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			73	5		78
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	73	5	0

Variants in GOLGA6C

This is a list of pathogenic ClinVar variants found in the GOLGA6C region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-75258627-A-C		not specified	Uncertain significance (Dec 07, 2021)
15-75260418-G-A		not specified	Uncertain significance (Mar 30, 2024)
15-75260475-G-T		not specified	Likely benign (Dec 07, 2021)
15-75260485-C-G		not specified	Uncertain significance (Mar 03, 2025)
15-75263359-G-T		not specified	Uncertain significance (Sep 27, 2022)
15-75263360-A-G		not specified	Uncertain significance (Jan 24, 2024)
15-75263364-A-C		not specified	Uncertain significance (Dec 21, 2023)
15-75263364-A-G		not specified	Uncertain significance (May 30, 2024)
15-75263649-C-A		not specified	Uncertain significance (Feb 15, 2023)
15-75263838-A-G		not specified	Uncertain significance (Nov 15, 2024)
15-75263859-C-T		not specified	Uncertain significance (Jun 03, 2025)
15-75263877-G-A		not specified	Uncertain significance (Nov 18, 2022)
15-75263977-A-T		not specified	Uncertain significance (May 16, 2025)
15-75264016-T-C		not specified	Uncertain significance (Apr 13, 2025)
15-75264019-A-C		not specified	Uncertain significance (Aug 30, 2021)
15-75264025-T-G		not specified	Uncertain significance (Dec 01, 2022)
15-75264029-A-T		not specified	Uncertain significance (Jan 18, 2025)
15-75264039-C-T		not specified	Uncertain significance (Apr 13, 2023)
15-75264040-G-A		not specified	Uncertain significance (Mar 14, 2025)
15-75264057-T-C		not specified	Uncertain significance (Mar 27, 2025)
15-75264066-C-G		not specified	Uncertain significance (Dec 14, 2023)
15-75264080-C-G		not specified	Uncertain significance (Jun 26, 2024)
15-75265151-G-C		not specified	Uncertain significance (Aug 12, 2021)
15-75265152-C-T		not specified	Uncertain significance (Apr 13, 2022)
15-75265153-G-A		not specified	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLGA6C	protein_coding	protein_coding	ENST00000300576	18	11601

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00100	0.830	120424	0	6	120430	0.0000249

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.11	153	119	1.29	0.00000674	4366
Missense in Polyphen		46	41.653	1.1044		1655
Synonymous	-0.461	55	50.8	1.08	0.00000325	1215
Loss of Function	1.18	6	10.0	0.598	4.82e-7	479

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000543	0.0000543
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: Golgi organization;spindle assembly
• Cellular component: Golgi cis cisterna;Golgi apparatus;cis-Golgi network;Golgi cisterna membrane